ISQ User Guide - Write Frame of Mind

4 Creating a Method
b. Set the MS Transfer Line Temperature. This field represents the temperature of the
transfer line, which is the tube that contains the column as it leaves the GC oven and
enters the ISQ. The maximum allowable temperature is 400 °C. However, you will
damage the column and contaminate the ISQ if you set the transfer line temperature
above the maximum allowed temperature of the column.
IMPORTANT You should always set the transfer line temperature in Xcalibur and NOT
through the GC.
c. Set the Ion Source Temperature. You can enter a value between 0 and 350 °C. The
optimal temperature depends on the analyte. Higher temperatures will keep the ion
source cleaner, but will lead to increased fragmentation, which may reduce sensitivity.
For most compounds, a source temperature of 200 °C (default) is adequate.
d. Select the Acquisition Threshold checkbox and enter a value for the minimum peak
height for the data file, if needed. If your peak has an intensity that is below this
threshold, it will not be stored. This setting may help reduce noise, but it may also
alter the reported isotope ratios because the smaller isotope signals will be
preferentially reduced.
e. Select EI from the Ionization Mode pull-down menu.
Note Only use CI if you have installed a CI ion volume in the ISQ and you have
connected CI reagent gas to your system. If you have CI, select a CI Gas Type from the
pull-down menu and set the CI Gas Flow. Typical values for NCI are 1.0 mL/min. For
PCI, the gas flows are typically 1.5 mL/min.
Thermo Scientific ISQ User Guide 35